├── .copier-answers.yml ├── .git_archival.txt ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── dependabot.yml ├── matchers │ └── pylint.json └── workflows │ ├── cd.yml │ ├── ci.yml │ └── pages.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── dev1 ├── convert_zarr_v2_to_v3 │ ├── __pycache__ │ │ └── util.cpython-310.pyc │ ├── convert_zarr_v2_to_v3.py │ ├── environmentv2_3.yml │ └── util.py ├── environment.yaml ├── environment_windows.yml └── resave.py ├── dev2 ├── .pre-commit-config.yaml ├── environment.yaml └── resave.py ├── dev3 ├── 2024-07-02 │ ├── example-metadata │ │ ├── min-specimen-biosample.json │ │ └── minimal.json │ ├── images │ │ ├── graph-min-specimen-biosample.svg │ │ └── graph-minimal.svg │ └── ro-crate-metadata-proposal.md └── zarr-crate │ ├── README.md │ ├── example_usage │ ├── create_fly_ro_crate_metadata.py │ ├── example_ro_crate │ │ ├── 0 │ │ │ └── example_file.txt │ │ └── ro-crate-metadata.json │ └── read_ro_crate.py │ ├── pyproject.toml │ └── zarr_crate │ ├── __init__.py │ ├── rembi_extension.py │ └── zarr_extension.py ├── docs ├── conf.py └── index.md ├── noxfile.py ├── ome2024-ngff-challenge ├── .gitignore ├── .vscode │ └── extensions.json ├── README.md ├── index.html ├── jsconfig.json ├── package-lock.json ├── package.json ├── public │ ├── check.png │ ├── copy.png │ ├── czi-logo-chan-zuckerberg-initiative-logo.png │ ├── favicon-16x16.png │ ├── github-mark-white.svg │ ├── idr-mark.svg │ ├── nfdi4bioimage.png │ ├── nfdi_rgb_Wortmarke_Zusatz_quer.png │ ├── ome-logomark.svg │ ├── ome-main-nav.svg │ ├── original-data.svg │ ├── selectCaret.svg │ ├── ssbd-logo.png │ └── vizarr_logo.png ├── src │ ├── About.svelte │ ├── App.svelte │ ├── ColumnSort.svelte │ ├── Header.svelte │ ├── ImageList.svelte │ ├── Main.svelte │ ├── Nav.svelte │ ├── PreviewPopup.svelte │ ├── SourcePanel.svelte │ ├── ThumbGallery.svelte │ ├── ThumbLoader.svelte │ ├── Thumbnail.svelte │ ├── ZarrListItem.svelte │ ├── app.css │ ├── main.js │ ├── ontologyStore.js │ ├── tableStore.js │ ├── util.js │ └── vite-env.d.ts └── vite.config.js ├── pyproject.toml ├── samples ├── crick.csv ├── ebi-ngff-challenge-samples.csv ├── flamingo.csv ├── fzj.csv ├── idr0004_samples.csv ├── idr0010_samples.csv ├── idr0011_samples.csv ├── idr0012_samples.csv ├── idr0013_samples.csv ├── idr0015_samples.csv ├── idr0016_samples.csv ├── idr0025_samples.csv ├── idr0026_samples.csv ├── idr0033_samples.csv ├── idr0035_samples.csv ├── idr0036_samples.csv ├── idr0044_samples.csv ├── idr0051_samples.csv ├── idr0054_samples.csv ├── idr0066_samples.csv ├── idr0090_samples.csv ├── idr0157_samples.csv ├── idr_samples.csv ├── jax_samples.csv ├── lin_samples.csv ├── load_zarr_stats.py ├── n4bi.csv ├── ngff_samples.csv ├── other_samples.csv ├── ssbd_samples.csv ├── uni_muenster_samples.csv └── webknossos_samples.csv ├── src └── ome2024_ngff_challenge │ ├── __init__.py │ ├── lookup.py │ ├── py.typed │ ├── resave.py │ ├── utils.py │ └── zarr_crate │ ├── __init__.py │ ├── rembi_extension.py │ └── zarr_extension.py └── tests ├── data ├── 2d.fake ├── 2d.fake.ini ├── 2d.zarr │ ├── 0 │ │ ├── 0 │ │ │ ├── 0 │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ ├── 1 │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ └── 2 │ │ │ │ └── 0 │ │ │ │ └── 0 │ │ │ │ └── 0 │ │ └── .zarray │ ├── .zattrs │ └── .zgroup ├── bf2raw.fake ├── bf2raw.fake.ini ├── bf2raw.zarr │ ├── 0 │ │ ├── 0 │ │ │ ├── 0 │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ └── .zarray │ │ ├── .zattrs │ │ └── .zgroup │ ├── 1 │ │ ├── 0 │ │ │ ├── 0 │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ │ │ └── 0 │ │ │ └── .zarray │ │ ├── .zattrs │ │ └── .zgroup │ ├── .zattrs │ ├── .zgroup │ └── OME │ │ ├── .zattrs │ │ ├── .zgroup │ │ └── METADATA.ome.xml ├── hcs.fake ├── hcs.fake.ini └── hcs.zarr │ ├── .zattrs │ ├── .zgroup │ ├── A │ ├── 1 │ │ ├── 0 │ │ │ ├── 0 │ │ │ │ ├── 0 │ │ │ │ │ ├── 0 │ │ │ │ │ │ └── 0 │ │ │ │ │ │ │ └── 0 │ │ │ │ │ │ │ └── 0 │ │ 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